Its a good idea to replace all the wear items in there: pilot bushing/bearing, throwout bearing, etc. You may want to check availability of an input shaft seal. Yours may be leaking.
There are pullers available for pilot bushings. Most auto parts stores offer them for rental. There are workarounds out there (grease and a punch, chisels, whatnot) but I can't say that I've ever tried them.
Bolts are a maybe. The torque spec doesn't come up with any torque to yield stuff, but if they're cheap I'd just replace them for piece of mind.
After some reading, it looks like you're right on the pilot bushing. I'm not sure how that works out with nothing supporting the end of the input shaft. I would think that such a design would lead to premature input shaft bearing failure. Maybe they use a second bearing inside the case or something?
I can't find anything on an input seal, but something has to seal the front of the transmission.
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